Characterization of the internal dynamics and conformational space of zinc-bound amyloid β peptides by replica-exchange molecular dynamics simulations

European Biophysics Journal ◽

10.1007/s00249-013-0906-0 ◽

2013 ◽

Vol 42 (7) ◽

pp. 575-586 ◽

Author(s):

Liang Xu ◽

Xiaojuan Wang ◽

Xicheng Wang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Conformational Space ◽

Replica Exchange ◽

Internal Dynamics ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25439 ◽

2017 ◽

Vol 86 (3) ◽

pp. 279-300 ◽

Author(s):

Charles R. Watts ◽

Andrew Gregory ◽

Cole Frisbie ◽

Sándor Lovas

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Force Fields ◽

Dynamic Properties ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent

Journal of Molecular Biology ◽

10.1016/j.jmb.2006.11.015 ◽

2007 ◽

Vol 366 (1) ◽

pp. 275-285 ◽

Author(s):

Andrij Baumketner ◽

Joan-Emma Shea

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent ◽

Dynamics Simulations

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Difference in dimer conformation between amyloid-β(1–42) and (1–43) proteins: Replica exchange molecular dynamics simulations in water

Chemical Physics Letters ◽

10.1016/j.cplett.2014.02.017 ◽

2014 ◽

Vol 595-596 ◽

pp. 242-249 ◽

Author(s):

Atsushi Yano ◽

Akisumi Okamoto ◽

Kazuya Nomura ◽

Shin’ichi Higai ◽

Noriyuki Kurita

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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Structures and Thermodynamics of Alzheimer’s Amyloid-β Aβ(16−35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length Aβ Fibrillation

The Journal of Physical Chemistry B ◽

10.1021/jp900425e ◽

2009 ◽

Vol 113 (21) ◽

pp. 7668-7675 ◽

Author(s):

Yassmine Chebaro ◽

Normand Mousseau ◽

Philippe Derreumaux

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Full Length ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-β Fragment 29−42 by Replica Exchange Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp110269a ◽

2011 ◽

Vol 115 (5) ◽

pp. 1282-1288 ◽

Author(s):

Yan Lu ◽

Guanghong Wei ◽

Philippe Derreumaux

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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Structural properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25270 ◽

2017 ◽

Vol 85 (6) ◽

pp. 1024-1045 ◽

Author(s):

Charles R. Watts ◽

Andrew J. Gregory ◽

Cole P. Frisbie ◽

Sándor Lovas

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Structural Properties ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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Faculty Opinions recommendation of Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1048003.498039 ◽

2006 ◽

Author(s):

D Peter Tieleman

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

K Channel ◽

Replica Exchange Molecular Dynamics ◽

X Ray ◽

X Ray Crystallography ◽

Dynamics Simulations

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Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

The Journal of Physical Chemistry B ◽

10.1021/jp802469g ◽

2008 ◽

Vol 112 (47) ◽

pp. 15064-15073 ◽

Author(s):

In-Chul Yeh ◽

Michael S. Lee ◽

Mark A. Olson

Keyword(s):

Molecular Dynamics ◽

Heat Capacity ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Implicit Solvent ◽

Replica Exchange Molecular Dynamics ◽

Solvent Models ◽

Dynamics Simulations ◽

Implicit Solvent Models

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3P314 Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulations(30.Miscellaneous topics,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.53.s264_1 ◽

2013 ◽

Vol 53 (supplement1-2) ◽

pp. S264

Author(s):

Shigehisa Watanabe ◽

Suyong Re ◽

Eiro Muneyuki ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Conformational Analysis ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Biophysical Society ◽

Dynamics Simulations

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Insights into the Folding and Unfolding Processes of Wild-Type and Mutated SH3 Domain by Molecular Dynamics and Replica Exchange Molecular Dynamics Simulations

PLoS ONE ◽

10.1371/journal.pone.0064886 ◽

2013 ◽

Vol 8 (5) ◽

pp. e64886 ◽

Author(s):

Wen-Ting Chu ◽

Ji-Long Zhang ◽

Qing-Chuan Zheng ◽

Lin Chen ◽

Hong-Xing Zhang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Wild Type ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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